ENST00000562621.1:n.3714C>G

Variant names:

• chr15-72752234-G-C
• rs9460
• ENST00000562621.1:n.3714C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000562621.1(ADPGK):​n.3714C>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.000000986 in 1,013,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 9.9e-7 (0 hom.)
• Consequence: ADPGK ENST00000562621.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.02
• Publications: 20 publications found

Genes affected

ADPGK (HGNC:25250): (ADP dependent glucokinase) ADPGK (EC 2.7.1.147) catalyzes the ADP-dependent phosphorylation of glucose to glucose-6-phosphate and may play a role in glycolysis, possibly during ischemic conditions (Ronimus and Morgan, 2004 [PubMed 14975750]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562621.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADPGK	NM_001365225.1	MANE Select	c.*107C>G		3_prime_UTR	Exon 7 of 7	NP_001352154.1
	ADPGK	NM_031284.5		c.*107C>G		3_prime_UTR	Exon 7 of 7	NP_112574.3
	ADPGK	NM_001365226.1		c.*107C>G		3_prime_UTR	Exon 7 of 7	NP_001352155.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADPGK	ENST00000562621.1	TSL:1	n.3714C>G		non_coding_transcript_exon	Exon 2 of 2
	ADPGK	ENST00000567941.5	TSL:1	n.*1574C>G		non_coding_transcript_exon	Exon 7 of 7	ENSP00000458102.1
	ADPGK	ENST00000569693.5	TSL:1	n.*875C>G		non_coding_transcript_exon	Exon 4 of 4	ENSP00000457572.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 9.86e-7 AC: 1 AN: 1013832 Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0 AN XY: 502556

African (AFR) AF: 0.00 AC: 0 AN: 22726

American (AMR) AF: 0.00 AC: 0 AN: 20658

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17414

East Asian (EAS) AF: 0.00 AC: 0 AN: 33870

South Asian (SAS) AF: 0.00 AC: 0 AN: 57106

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36126

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3144

European-Non Finnish (NFE) AF: 0.00000128 AC: 1 AN: 778330

Other (OTH) AF: 0.00 AC: 0 AN: 44458

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 83644

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	18
DANN	Benign	0.89
PhyloP100		4.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9460; hg19: chr15-73044575;